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Samtools coverage submodule #2356

Merged
merged 10 commits into from Feb 23, 2024
Merged

Samtools coverage submodule #2356

merged 10 commits into from Feb 23, 2024

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vladsavelyev
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Parse samtools coverage output:

#rname  startpos  endpos  numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
chr1           1   40001      5640      1181  2.95243   16.7743    40.9             60
chr2           1   40001      5640      1181  2.95243   16.7743    40.9             60

Adds:

  • Line plot with regions along the x-axis, and metrics as a switch button panel,
  • Table/violin summing/averaging across all regions,
  • "Mean Depth" in gen stats.
Screenshot 2024-02-20 at 14 41 35

Fixes #2021

@vladsavelyev vladsavelyev added awaits-review Awaiting final review and merge. module: enhancement labels Feb 20, 2024
vladsavelyev added a commit to MultiQC/test-data that referenced this pull request Feb 20, 2024
@vladsavelyev
Samtools coverage (MultiQC/MultiQC#2356)
a2d5aff
@vladsavelyev vladsavelyev mentioned this pull request Feb 20, 2024
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@multiqc-bot changelog

@vladsavelyev vladsavelyev removed the awaits-review Awaiting final review and merge. label Feb 20, 2024
@vladsavelyev vladsavelyev added the awaits-review Awaiting final review and merge. label Feb 22, 2024
@ewels
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ewels commented Feb 23, 2024

I get an exciting error:

$ multiqc -f .

  /// MultiQC 🔍 | v1.20 (71ac39a)

|           multiqc | Search path : /Users/ewels/GitHub/MultiQC/test-data/data/modules/samtools/coverage
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 3/3
/Users/ewels/GitHub/MultiQC/MultiQC/multiqc/modules/samtools/rmdup.py:20: SyntaxWarning: invalid escape sequence '\['
  dups_regex = "\[bam_rmdups?e?_core\] (\d+) / (\d+) = (\d+\.\d+) in library '(.*)'"
|          samtools | Found 3 coverage reports
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | MultiQC complete

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ewels commented Feb 23, 2024

Seems unrelated to this PR.. Get the same thing on main

ewels
ewels approved these changes Feb 23, 2024
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LGTM! Would be good to clean up the regex escape thing, but otherwise good to merge.

vladsavelyev and others added 2 commits February 23, 2024 12:06
@vladsavelyev @ewels
Update multiqc/modules/samtools/rmdup.py
7fc5484 
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
@vladsavelyev
Fix rmdup regex
061fe29
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Fixed the warning 👍

@vladsavelyev vladsavelyev merged commit 4630828 into main Feb 23, 2024
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@vladsavelyev vladsavelyev deleted the samtools-coverage branch February 23, 2024 11:09
vladsavelyev added a commit that referenced this pull request Feb 23, 2024
@vladsavelyev @multiqc-bot @ewels
Samtools coverage submodule (#2356)
41afe76 
* Allow override title per-dataset

* Add samtools coverage submodule

* [automated] Update CHANGELOG.md

* Fix changelog

* Update multiqc/modules/samtools/rmdup.py

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Fix rmdup regex

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
ewels added a commit that referenced this pull request Feb 24, 2024
@ewels @vladsavelyev @multiqc-bot
Versions API (#2092)
cce7616 
* Rewrite version checker to use new API endpoint

* Move version_check_url into the config, for local testing

* Version check URL

* Clean up

* Typo

* Parse CI env var

* Fix

* Catch timeout error

* UMI-tools: support `extract` command (#2296)

* UMI-tools: support extract command

* [automated] Update CHANGELOG.md

* Add barplot

* Barplot with extract stats

* Doc

* Changelog

* Lint

* Fix duplicated IDs in linting

* Merge conflict

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Infinite dmax or dmin fail JSON dump load in JavaScript (#2354)

* Infinite dmax or dmin fail JSON dump load in JavaScript

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Fix changelog.py for module updates

* Whatshap: robust to stdout appended to TSV (#2361)

* Drop `full_figure_for_development` the call to avoid Kaleido issues (#2359)

* Wrap `full_figure_for_development` in try-except to handle Kaleido errors

* [automated] Update CHANGELOG.md

* Get around read-only /tmp

* Remove the full_figure_for_development call for good, just re-calcualte range from data

* Changelog

* Comments

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* PURPLE: support v4.0.1 output without `version` column (#2366)

* Purple: support v4.0.1 output without version column

* [automated] Update CHANGELOG.md

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Ignore `.parquet` files. More robust `htseq` file reading loop (#2364)

* Ignore .parquet files. Handle htseq unicode errors

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Add box plot (#2358)

* Add box plot

* [automated] Update CHANGELOG.md

* Fix linting

* CSP

* Fix sample order

* Allow overriding title for a dataset tab

* Violin: color dots blue in monochrome violins to indiciate interactivity

* Mono color for boxes, support highliting

* Rename beeswarm to violin

* Barplot: stacking: normal should mean stacked, not grouped

* Update plotting documentation

* Docs

* Redirect beeswarm

* CSP

* Update the flat plot section and remove highcharts mention

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Replace `setup.py` with `pyproject.toml` (#2353)

* Replace setup.py with pyproject.toml

* [automated] Update CHANGELOG.md

* Add myself as author

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Put matplotlib back into main deps (#2370)

* Put matplotlib back into main deps

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>

* Generic font family for Plotly (#2368)

* Generic font family for Plotly

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Samtools `coverage` submodule (#2356)

* Allow override title per-dataset

* Add samtools coverage submodule

* [automated] Update CHANGELOG.md

* Fix changelog

* Update multiqc/modules/samtools/rmdup.py

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Fix rmdup regex

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Update `modules.md`: `pyproject.toml`, `"shared_key": "read_count"`, ruffify (#2371)

* Update modules.md: `pyproject.toml`, `"shared_key": "read_count"`, ruffify

* [automated] Update CHANGELOG.md

* Apply suggestions from code review

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

---------

Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com>
Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
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Samtools coverage output
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